Antigen Tracking Figures
Ryan Sheridan
2024-01-05
Figure 1
Antigen persists in discrete cell populations within the lymph node
- Experimental design
- Mean Ag-score is shown for each cell type for 2, 14, 21, and 42 days post vaccination.
- UMAP projection shows LEC subsets.
- UMAP projections show Ag-scores for LEC subsets for each timepoint.
- Mean Ag-score is shown for LEC subsets for each timepoint.
- Ag-scores are shown for each timepoint for each LEC subset.
- UMAP projection shows DC subsets.
- UMAP projections show Ag-scores for DC subsets for each timepoint.
- Mean Ag-score is shown for DC subsets for each timepoint.
- Ag-scores are shown for each timepoint for each DC subset.
Notes
- Experiment 1 is shown for the LEC 21 and 42 day timepoints. Experiment 2 data include very few LECs for the 21 day timepoint.
- Experiment 2 is shown for the DC 21 and 42 day timepoints. Experiment 1 data are lower quality (sparse signal, mostly zeros).
- Subsets are only shown if there are >= 5 cells for each timepoint
- CD45+ and CD45- cell types are only shown for the CD45+ and CD45- datasets, respectively.
Figure S1
- UMAP projections show cell types identified for CD45- and CD45+ samples.
- Ag-scores are shown for each timepoint for each LEC subset. Two biological replicates are shown for the day 21 and day 42 timepoints. The number of cells identified for each LEC subset is shown above each timepoint.
- Ag-scores are shown for each timepoint fo each DC subset, as described in B.
Figure 2
Identification of an antigen archiving gene signature
- Ag-score is shown for day 14 Ag-high and -low cells identified for LEC subsets with the highest Ag-score.
- The fraction of cells predicted to be Ag-competent is shown for each LEC subset 14, 21, and 42 days post vaccination.
- Ag-high module score is shown for Ag-high and predicted Ag-competent LECs for each timepoint. P values were calculated by pooling cells from all three timepoints for each Ag class. P values were calculated using a one-sided t test with Bonferroni correction to compare Ag-high vs Ag-competent and Ag-competent vs Ag-low cells for each LEC subset.
- UMAP projections show cLEC Ag-high module scores for each timepoint.
- The expression of select genes from the Ag-high (top four) and Ag-low (bottom four) gene modules is shown for cLECs. Genes identified as top predictors for all three LEC subsets are shown.
Notes
- Ag-low and -high cells were identified by separately clustering each d14 LEC subset for each sample into two groups based on Ag-score.
- The cutoffs identified for the d14 dataset were then used to identify Ag-high cells for the other timepoints.
- With this approach there is a different cutoff for each LEC subset, but the cutoff is consistent across timepoints.
